Copyright 2025 Laboratory Automation Solutions info@labsolns.com

This file is part of LIMS*Nucleus.

LIMS*Nucleus can not be copied and/or distributed without the express permission of Laboratory Automation Solutions

This project is not open source, but source code is available to licensees.
You are not allowed to redistribute this project with “enhancements” i.e. fork.
You may modify this project to suit your needs, but must retain the modified code within your organization.
You cannot commercialize this project.

A perpetual license (₿0.010 BTC) provides:

• all future upgrades
• bug fixes
• support
• source code

Register here

Free license to academics who register with an .edu email

For more information contact: info@labsolns.com

LIMS*Nucleus is a software program used to manage multi-well plates in an academic or industrial environment. Functionality includes:

• Generate 96, 384 or 1536 well plates with or without samples
• Collect plates into plate sets
• Group or split plate sets
• Reformat plates - four 96 well plates into a 384 well plate; four 384 well plates into a 1536 well plate
• Associate assay data with plate sets
• Identify hits scoring in assays using included algorithms - or write your own
• Export annotated data
• Generate worklists for liquid handling robots
• Rearray hits into a smaller collection of plates
• Prototype algorithms, visualization with R/Shiny
• Create assay development workflows
• Standardize and capture process details
• Up and running without an RFOP (room full of programmers)
• Hand coded!
• Evaluate an online instance
• Video overviews of features and capabilities

LIMS*Nucleus has a restricted set of features - multi-well plate management, hit identification, rearraying - and serves as the core of a larger system. Source code is available for modification. The architecture is simple client/server with no middleware or ORM. The client utilizes Bootstrap/Datatables and the database is PostgreSQL The software is packaged as a Guix pack for easy installation/configuration. R/Shiny dashboards can be used to extend functionality.

Next: Monoliths vs Systems

File characteristics

Tab delimitted ASCII text Header required Column names must be all lower case Column name spelling is critical Column order is critical

Data import

Plate order is defined by the plate set. Import plates must be in the same order as the plate set

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plate	well	response
1	1	0.293825508745667
1	2	0.114021462999455
1	3	0.238314598659791
1	4	0.396061216051141
1	5	0.296039032793309
1	6	0.442385430319253

Accession ID import

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plate	well	accs.id
1	1	AMRVK5473H
1	2	KMNCX9294W
1	3	EHRXZ2102Z
1	4	COZHR7852Q
1	5	FJVNR6433Q
1	6	WTCKQ4682U

Barcode ID import

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plate 	barcode.id
1	LN000001
2	LN000002
3	LN000003
4	LN000004
5	LN000005
6	LN000006
7	LN000007
8	LN000008
9	LN000009
10	LN000010

Bulk target import

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project	target 	description	accession
1	muCD71	Mouse transferrin receptor	FHD8SU29
1	huCD71	Human transferrin receptor	JDHSU789
1	cynoCD71	Monkey transferrin receptor	KSIOW8H3
1	BSA	Bovine serum albumin	KEUI87YH
2	Lysozyme	Lysozyme	KDJFG98D
2	GAPDH	Glyceraldehyde Phosphate Dehydrogenase	KFIIOD09
2	ICAM4	ICAM 4 integrin	KL0OIE7U
2	IL21R	IL21 receptor	KOI89IUY

Multiple workflows use a file import form show below. Text provides instructions as well as an example of what the contents of the file should look like. Import files are always tab delimitted plain text. Column order, spelling and capitalization are critical:

Post file selection trucated contents of the import file are displayed for confirmation prior to submission. If file contents are determined to be incompatible with requirements for a particlar import e.g. wrong number of rows/columns, incorrect header, a warning will be issued:

Only plate sets can be grouped. Navigate into the project of interest containing the plate sets to be grouped and highlight the plate sets. Select Utilities/Group from the menu bar:

A dialog will open. Fill in the name and description for the new plate sets. The source plate sets must be of the same format and layout, which will be indicated in the dialog box. Select a plate type and press OK.

View the channels video for details on how to set up a Guix channel.

• Installation

labsolns can be installed as a Guix channel. To do so, add it to ~/.config/guix/channels.scm:

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(cons* (channel
        (name 'labsolns)
        (url "https://github.com/mbcladwell/labsolns")
        (branch "master")
        ;; Enable signature verification:
        (introduction
         (make-channel-introduction
          "74b2041a467ce3e35fd989f2d66a08e5697f980b"
          (openpgp-fingerprint
           "E709 94D1 9CB0 FE2B CAC4  9E54 0BF8 F292 4D2B 1944"))))
       %default-channels)

Then run guix pull.

If you receive error messages like “…commit nnnn is not a descendant of nnnnn …” use

guix pull –allow-downgrades.

Hit identification can be accomplished using one of three different methods:

1. Select an algorithm during data import

Select an algorithm from the drop down during data import. Hits will be identified and the Hit List name and description text fields will be enabled so you can register the hit list.

2. In the scatterplot/replot view, view and generate a hit list

When plotting or replotting, the tool icon provides the option to view a hit list. The hit list view provides the option to register and save the hit list.

3. Export data and use external data analysis to identify hits. Import the hit list.

Post data import, annotated data can be exported for visualization using other software. A hit list can be compiled external to LIMS*Nucleus and then imported.

Scroll down to the hit list and import under the tools icon:

Invalid registration information.
Wallet/Customer ID not generated.

Try again.

Cloud

Contact Mortimer Cladwell and request a dedicated AWS instance running a fully functional copy of LIMS*Nucleus for evaluation.

username: demo
password: demo

Install on AWS EC2

Install your own personal instance on Amazon following directions provided here. This method installs Guix, sets up a guix channel, and pulls the LIMS*Nucleus software. Requires a t2.medium instance on AWS.

Install using a Guix Pack

For users not interested in the Guix package manager, LIMS*Nucleus and all its dependencies have been collected in a Guix Pack. You can use this install script to install the LIMS*Nucleus client and optionally the database. Suitable for use with the t2.micro free tier instance of Debian on AWS or local installation. This will be the best option for most users. Follow the video here. Detailed step by step manual installation instructions with troubleshooting tips here.

Install on Windows 11 wsl2

Windows 11

LIMS*Nucleus example database contains plate sets, plates, hit list, assay runs and data. The various projects are at different stages of completion to demonstrate the functionality of the application.

### Files for import

Provide your own import files or use the supplied data below:

Statistics for example assay data files